Self−assemble donor−acceptor chromophores have extensive applications in photofunctional devices owing to their unique charge transport properties. To explore the possibility of improving nonlinear optical (NLO) properties by self-assembling to multilayer complexes, we theoretically investigated the geometric and electronic structures, interlayer weak interactions, absorption spectra, charge transfer properties, polarizabilities (α) and first hyperpolarizabilities (β) of naphthalimide, -phenyl and -naphthyl monomers, dimers and trimers by increasing the layer number n (n = 1, 2, 3). Different stacking patterns of their dimers were also taken into account. It shows that parallel stacking patterns are conducive to maximizing overlap with respect to antiparallel ones due to the concept of optimal π-orbital overlap is more vast than purely maximizing cofacial overlap to improve charge transport. The decreases in band gap for the di/trimeric vs monomeric naphthalimide, -phenyl and -naphthyl monomers indicate the possibility of more favorable photoinduced electron transition in the aggregate when compared to the monomer. The linear and second order NLO properties of these complexes are investigated in detail. The α values increase linearly as the increase number n of layer (n=1, 2 and 3), providing a new kind of tendency forecast method for the linear optical properties. Along with the increasing electron donating ability of the donor, the βtot values of monomers increased, revealing the general rule of designing NLO moleculars. The dependence of βtot value on the layer number shows that the βtot value increased with the increased number of layer, which can be rationalized by considering the enhancement of interlayer electronic transition and two-dimensional NLO character with the two charge transfer axes. We hope this work may evoke one’s attention to design new, highly efficient second-order NLO materials with excellent building blocks: multilayer complexes.